annovarR (version 1.0.0)

sqlite.build: Build annovarR database in sqlite

Description

Build annovarR database in sqlite

Usage

sqlite.build(filename = NULL, sqlite.connect.params = list(dbname = "",
  table.name = ""), dat = data.table(), fread.params = list(),
  new.colnames = NULL, overwrite = TRUE, verbose = FALSE, ...)

Arguments

filename

Path of raw data, will be read by fread

sqlite.connect.params

Connect to sqlite database params [dbname, table.name]

dat

Object of data.table, as the input data to build database (optional)

fread.params

Other parameters be used in fread

new.colnames

New colnames of table, default is to retain the original

overwrite

Ligical indicating wheather overwrite sqlite database

verbose

Ligical indicating wheather show the log message

...

Other parameters be used in dbWriteTable

Examples

# NOT RUN {
test.dat <- system.file('extdata', 'demo/sqlite.dat.txt', package = 'annovarR')
test.sqlite <- sprintf('%s/snp.test.sqlite', tempdir())
x <- sqlite.build(filename = test.dat, list(dbname = test.sqlite, 
table.name = 'snp_test'))
test.sqlite <- normalizePath(test.sqlite, '/')
file.remove(test.sqlite)
# }